Format code with black and isort

datasets/Appenzeller-Herzog_2019/compose.py

@@ -19,12 +19,16 @@
 
 # adjust columns and drop missing and duplicate ids
 df["doi"] = "https://doi.org/" + df["doi"].str.extract(r"(10.\S+)")
-df["pmid"] = "https://pubmed.ncbi.nlm.nih.gov/" + df["url"].str.extract(r"id\=pmid\:(\d+)")
+df["pmid"] = "https://pubmed.ncbi.nlm.nih.gov/" + df["url"].str.extract(
+ r"id\=pmid\:(\d+)"
+)
 
 # save results to file
 df.to_csv(f"{key}_raw.csv", index=False)
 
 df_new = df[["doi", "pmid", "label_included"]].copy()
 df_new["openalex_id"] = None
 
-df_new[["doi", "pmid", "openalex_id", "label_included"]].to_csv(f"{key}_ids.csv", index=False)
+df_new[["doi", "pmid", "openalex_id", "label_included"]].to_csv(
+ f"{key}_ids.csv", index=False
+)

datasets/Bannach-Brown_2019/compose.py

@@ -13,12 +13,16 @@
 
 # adjust columns
 df["doi"] = "https://doi.org/" + df["url"].str.extract(r"(10.\S+)")
-df["pmid"] = "https://pubmed.ncbi.nlm.nih.gov/" + df["url"].str.extract(r"gov\/pubmed\/(\d+)")
+df["pmid"] = "https://pubmed.ncbi.nlm.nih.gov/" + df["url"].str.extract(
+ r"gov\/pubmed\/(\d+)"
+)
 
 # export
 df.to_csv(f"{key}_raw.csv", index=False)
 
 df_new = df[["doi", "pmid", "label_included"]].copy()
 df_new["openalex_id"] = None
 
-df_new[["doi", "pmid", "openalex_id", "label_included"]].to_csv(f"{key}_ids.csv", index=False)
+df_new[["doi", "pmid", "openalex_id", "label_included"]].to_csv(
+ f"{key}_ids.csv", index=False
+)

datasets/Bos_2018/Bos_2018_ids.csv

@@ -661,8 +661,8 @@ https://pubmed.ncbi.nlm.nih.gov/22241387,https://doi.org/10.3174/ajnr.a2868,http
 https://pubmed.ncbi.nlm.nih.gov/22918430,https://doi.org/10.3174/ajnr.a3303,https://openalex.org/W2162307137,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/19541689,https://doi.org/10.1136/jnnp.2008.158881,https://openalex.org/W2171487159,0,id_retrieval_pmid
 ,https://doi.org/10.1002/mp.12328,https://openalex.org/W2613536437,0,id_retrieval_doi
-https://pubmed.ncbi.nlm.nih.gov/27243267,,,0,
-https://pubmed.ncbi.nlm.nih.gov/27243267,,,0,
+https://pubmed.ncbi.nlm.nih.gov/27243267,https://doi.org/10.1148/radiol.2016152244,https://openalex.org/W2415637550,0,search_title_year
+https://pubmed.ncbi.nlm.nih.gov/27243267,https://doi.org/10.1148/radiol.2016152244,https://openalex.org/W2415637550,0,search_title_year
 https://pubmed.ncbi.nlm.nih.gov/25468879,https://doi.org/10.1161/strokeaha.114.007568,https://openalex.org/W2134467108,0,id_retrieval_pmid
 ,https://doi.org/10.3174/ajnr.a4828,https://openalex.org/W2414567120,0,id_retrieval_doi
 https://pubmed.ncbi.nlm.nih.gov/27282862,https://doi.org/10.3174/ajnr.a4828,https://openalex.org/W2414567120,0,id_retrieval_pmid
@@ -724,7 +724,7 @@ https://pubmed.ncbi.nlm.nih.gov/14718359,https://doi.org/10.1161/01.hyp.00001123
 https://pubmed.ncbi.nlm.nih.gov/19597086,https://doi.org/10.1001/archneurol.2009.110,https://openalex.org/W2106449289,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/17903882,https://doi.org/10.1053/jscd.2002.129597,https://openalex.org/W2055898278,0,id_retrieval_pmid
 ,,,0,
-https://pubmed.ncbi.nlm.nih.gov/27643255,,,0,
+https://pubmed.ncbi.nlm.nih.gov/27643255,https://doi.org/10.1097/01.hjh.0000499884.77354.0e,https://openalex.org/W2519695654,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/15017012,https://doi.org/10.1161/01.str.0000124124.69842.2d,https://openalex.org/W2099444565,0,id_retrieval_pmid
 ,,,0,
 https://pubmed.ncbi.nlm.nih.gov/29289936,https://doi.org/10.1136/bmjopen-2017-018328,https://openalex.org/W2776273648,0,id_retrieval_pmid
@@ -1015,7 +1015,7 @@ https://pubmed.ncbi.nlm.nih.gov/25707397,https://doi.org/10.1038/mp.2015.1,https
 ,https://doi.org/10.1016/j.parkreldis.2012.03.008,https://openalex.org/W2034026137,0,search_title
 ,,,0,
 ,https://doi.org/10.1038/mp.2016.19,https://openalex.org/W2306346388,0,id_retrieval_doi
-https://pubmed.ncbi.nlm.nih.gov/27001615,,,0,
+https://pubmed.ncbi.nlm.nih.gov/27001615,https://doi.org/10.1038/mp.2016.19,https://openalex.org/W2306346388,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/24661277,https://doi.org/10.1111/ene.12412,https://openalex.org/W2033891585,0,id_retrieval_pmid
 ,https://doi.org/10.1007/bf00313646,https://openalex.org/W1991847110,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/19280875,,https://openalex.org/W2272252746,0,id_retrieval_pmid
@@ -1051,7 +1051,7 @@ https://pubmed.ncbi.nlm.nih.gov/29213788,https://doi.org/10.1590/s1980-57642012d
 ,https://doi.org/10.1159/000355683,https://openalex.org/W2007177191,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/26410118,https://doi.org/10.3233/thc-151012,https://openalex.org/W1223013076,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/9040729,https://doi.org/10.1212/wnl.48.2.399,https://openalex.org/W1986652867,0,id_retrieval_pmid
-https://pubmed.ncbi.nlm.nih.gov/27010959,,,0,
+https://pubmed.ncbi.nlm.nih.gov/27010959,https://doi.org/10.1371/journal.pone.0152082,https://openalex.org/W2316313792,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/26691551,https://doi.org/10.1097/qad.0000000000000945,https://openalex.org/W2473007096,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/17895210,https://doi.org/10.1053/jscd.2000.5869,https://openalex.org/W2154612925,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/25690257,https://doi.org/10.1002/mds.26118,https://openalex.org/W1834161563,0,id_retrieval_pmid
@@ -1631,7 +1631,7 @@ https://pubmed.ncbi.nlm.nih.gov/10990518,https://doi.org/10.1136/jnnp.69.4.528,h
 https://pubmed.ncbi.nlm.nih.gov/16755582,https://doi.org/10.1002/mds.20979,https://openalex.org/W2006952111,0,id_retrieval_pmid
 ,https://doi.org/10.1002/mds.23762,https://openalex.org/W2144474092,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/19850138,https://doi.org/10.1016/j.neuroimage.2009.10.015,https://openalex.org/W2028362961,0,id_retrieval_pmid
-https://pubmed.ncbi.nlm.nih.gov/12771251,,,0,
+https://pubmed.ncbi.nlm.nih.gov/12771251,https://doi.org/10.1212/01.wnl.0000065888.88988.6e,https://openalex.org/W1995119071,0,search_title_year
 ,https://doi.org/10.1093/gerona/glq038,https://openalex.org/W2137245572,0,search_title
 ,https://doi.org/10.1093/ageing/afr113,https://openalex.org/W1966821136,0,search_title
 ,https://doi.org/10.1111/j.1532-5415.2005.53208.x,https://openalex.org/W2112924247,0,search_title
@@ -2345,7 +2345,7 @@ https://pubmed.ncbi.nlm.nih.gov/25748008,https://doi.org/10.6009/jjrt.2015_jsrt_
 https://pubmed.ncbi.nlm.nih.gov/24212919,https://doi.org/10.1093/ageing/aft175,https://openalex.org/W2149055962,0,id_retrieval_pmid
 ,https://doi.org/10.1136/jnnp.67.6.811,https://openalex.org/W1997982282,0,search_title
 ,https://doi.org/10.1001/archneur.61.6.946,https://openalex.org/W2074137222,0,search_title
-https://pubmed.ncbi.nlm.nih.gov/12297568,,,0,
+https://pubmed.ncbi.nlm.nih.gov/12297568,https://doi.org/10.1212/wnl.59.6.867,https://openalex.org/W2117648794,0,search_title_year
 https://pubmed.ncbi.nlm.nih.gov/19290743,https://doi.org/10.1037/a0013421,https://openalex.org/W1995138617,0,id_retrieval_pmid
 ,https://doi.org/10.1212/wnl.57.12.2229,https://openalex.org/W2120962895,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/16116117,https://doi.org/10.1212/01.wnl.0000172913.88973.0d,https://openalex.org/W2035228196,0,id_retrieval_pmid
@@ -2677,7 +2677,7 @@ https://pubmed.ncbi.nlm.nih.gov/27997036,https://doi.org/10.1002/ana.24844,https
 https://pubmed.ncbi.nlm.nih.gov/22459725,,https://openalex.org/W2413780474,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/26899579,https://doi.org/10.2174/1567205013666160222112634,https://openalex.org/W2277956342,0,id_retrieval_pmid
 ,https://doi.org/10.1212/wnl.0000000000002352,https://openalex.org/W2228844435,0,id_retrieval_doi
-https://pubmed.ncbi.nlm.nih.gov/12395806,,,0,
+https://pubmed.ncbi.nlm.nih.gov/12395806,https://doi.org/10.1212/wnl.59.8.1134,https://openalex.org/W2149213267,0,search_title_year
 ,,,0,
 https://pubmed.ncbi.nlm.nih.gov/29311653,https://doi.org/10.1038/s41380-017-0008-y,https://openalex.org/W2783984519,0,id_retrieval_pmid
 ,https://doi.org/10.1590/s0004-282x2007000300005,https://openalex.org/W2045418203,0,search_title
@@ -2935,7 +2935,7 @@ https://pubmed.ncbi.nlm.nih.gov/24433704,https://doi.org/10.1016/j.acra.2013.12.
 ,https://doi.org/10.1097/wad.0b013e3181df1c7b,https://openalex.org/W2058779405,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/26924981,https://doi.org/10.3389/fnagi.2016.00027,https://openalex.org/W2286849707,0,id_retrieval_pmid
 ,https://doi.org/10.1038/npp.2015.1,https://openalex.org/W2053868589,0,id_retrieval_doi
-https://pubmed.ncbi.nlm.nih.gov/25598427,,,0,
+https://pubmed.ncbi.nlm.nih.gov/25598427,https://doi.org/10.1038/npp.2015.1,https://openalex.org/W2053868589,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/25731624,https://doi.org/10.2174/1567205012666150302155336,https://openalex.org/W2158050756,0,id_retrieval_pmid
 ,,,0,
 ,https://doi.org/10.1186/1129-2377-14-98,https://openalex.org/W2063461108,0,search_title
@@ -3342,7 +3342,7 @@ https://pubmed.ncbi.nlm.nih.gov/23183589,https://doi.org/10.1159/000345184,https
 ,https://doi.org/10.1111/j.1440-1789.2008.00898.x,https://openalex.org/W2019220045,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/28000005,https://doi.org/10.1007/s00415-016-8362-2,https://openalex.org/W2566141743,0,id_retrieval_pmid
 ,,https://openalex.org/W10293438,0,search_title
-https://pubmed.ncbi.nlm.nih.gov/19349602,,,0,
+https://pubmed.ncbi.nlm.nih.gov/19349602,https://doi.org/10.1212/wnl.0b013e3181c77627,https://openalex.org/W4243646318,0,search_title_year
 https://pubmed.ncbi.nlm.nih.gov/18313775,https://doi.org/10.1016/j.archger.2008.01.010,https://openalex.org/W2052531369,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/28507298,https://doi.org/10.1038/s41598-017-02046-y,https://openalex.org/W2612470344,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/25603760,https://doi.org/10.1111/ene.12645,https://openalex.org/W2147988615,0,id_retrieval_pmid
@@ -3756,7 +3756,7 @@ https://pubmed.ncbi.nlm.nih.gov/19591295,,https://openalex.org/W2405129433,0,id_
 https://pubmed.ncbi.nlm.nih.gov/25756991,https://doi.org/10.1371/journal.pone.0120197,https://openalex.org/W1967811789,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/20007724,https://doi.org/10.3174/ajnr.a1860,https://openalex.org/W2140701635,0,id_retrieval_pmid
 ,https://doi.org/10.1159/000331450,https://openalex.org/W2001564332,0,search_title
-https://pubmed.ncbi.nlm.nih.gov/28278822,,,0,
+https://pubmed.ncbi.nlm.nih.gov/28278822,https://doi.org/10.1071/rdv29n1ab25,https://openalex.org/W2558878245,0,search_title
 https://pubmed.ncbi.nlm.nih.gov/28316870,https://doi.org/10.5469/neuroint.2017.12.1.50,https://openalex.org/W2606583025,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/27487889,https://doi.org/10.1118/1.4958959,https://openalex.org/W2499166316,0,id_retrieval_pmid
 ,https://doi.org/10.1002/ana.410380517,https://openalex.org/W2108277265,0,search_title
@@ -4599,7 +4599,7 @@ https://pubmed.ncbi.nlm.nih.gov/19332141,https://doi.org/10.1016/j.neuroimage.20
 https://pubmed.ncbi.nlm.nih.gov/22415749,https://doi.org/10.1002/gps.3791,https://openalex.org/W1489648828,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/19721847,,https://openalex.org/W132371621,0,id_retrieval_pmid
 ,https://doi.org/10.1177/153331750401900506,https://openalex.org/W2148178457,0,search_title
-https://pubmed.ncbi.nlm.nih.gov/23390180,,,0,
+https://pubmed.ncbi.nlm.nih.gov/23390180,https://doi.org/10.1212/wnl.0b013e31828407bc,https://openalex.org/W2099880194,0,search_title_year
 ,,https://openalex.org/W168328204,0,search_title
 ,,,0,
 ,,,0,
@@ -4697,7 +4697,7 @@ https://pubmed.ncbi.nlm.nih.gov/23290436,https://doi.org/10.1016/j.jstrokecerebr
 https://pubmed.ncbi.nlm.nih.gov/23254639,https://doi.org/10.3233/jad-122095,https://openalex.org/W1660239796,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/25153085,https://doi.org/10.1371/journal.pone.0106062,https://openalex.org/W2057413482,0,id_retrieval_pmid
 https://pubmed.ncbi.nlm.nih.gov/19068502,https://doi.org/10.1097/wad.0b013e318185e7fe,https://openalex.org/W2025489489,0,id_retrieval_pmid
-https://pubmed.ncbi.nlm.nih.gov/15277612,,,0,
+https://pubmed.ncbi.nlm.nih.gov/15277612,https://doi.org/10.1212/01.wnl.0000130531.90205.ef,https://openalex.org/W2040048921,0,search_title_year
 https://pubmed.ncbi.nlm.nih.gov/11295996,https://doi.org/10.1001/archneur.58.4.643,https://openalex.org/W2035813868,0,id_retrieval_pmid
 ,https://doi.org/10.1136/jnnp.60.2.158,https://openalex.org/W2162134958,0,search_title
 ,,https://openalex.org/W2389264091,0,search_title

datasets/Bos_2018/compose.py

@@ -17,13 +17,19 @@
 df["doi"] = "https://doi.org/" + df["doi"].str.extract(r"(10.\S+)")
 
 df["pmid"] = None
-pubmed = df["accession_number"].notnull() & (df["accession_number"].str.startswith("CN") == False)
-df.loc[pubmed, "pmid"] = "https://pubmed.ncbi.nlm.nih.gov/" + df.loc[pubmed, "accession_number"]
+pubmed = df["accession_number"].notnull() & (
+ df["accession_number"].str.startswith("CN") == False
+)
+df.loc[pubmed, "pmid"] = (
+ "https://pubmed.ncbi.nlm.nih.gov/" + df.loc[pubmed, "accession_number"]
+)
 
 # save results to file
 df.to_csv(f"{key}_raw.csv", index=False)
 
 df_new = df[["pmid", "doi", "label_included"]].copy()
 df_new["openalex_id"] = None
 
-df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv(f"{key}_ids.csv", index=False)
+df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv(
+ f"{key}_ids.csv", index=False
+)

datasets/Cohen_2006/compose.py

@@ -3,8 +3,6 @@
 import pandas as pd
 import requests
 
-
-
 if __name__ == "__main__":
 
  parser = argparse.ArgumentParser(prog="Compose Cohen data")
@@ -29,7 +27,9 @@
  df["doi"] = None
  df["openalex_id"] = None
 
- export_fp = f"{args.name}_ids.csv" if args.name else f"Cohen_2006_{args.subset}_ids.csv"
+ export_fp = (
+ f"{args.name}_ids.csv" if args.name else f"Cohen_2006_{args.subset}_ids.csv"
+ )
 
  # save results to file
  df[df["disease"] == args.subset][

datasets/Howard_2016/compose.py

@@ -11,8 +11,9 @@
 
 df_new = df_bpa[["pmid", "doi", "label_included"]].copy()
 df_new["openalex_id"] = None
-df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv("Wassenaar_2017_ids.csv", index=False)
-
+df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv(
+ "Wassenaar_2017_ids.csv", index=False
+)
 
 
 df_pfos = pd.read_excel(url, sheet_name="PFOS-PFOA")
@@ -24,7 +25,9 @@
 
 df_new = df_pfos[["pmid", "doi", "label_included"]].copy()
 df_new["openalex_id"] = None
-df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv("Rooney_2015_ids.csv", index=False)
+df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv(
+ "Rooney_2015_ids.csv", index=False
+)
 
 df_trans = pd.read_excel(url, sheet_name="Transgenerational")
 df_trans["label_included"] = df_trans["Status"].replace({"Excluded": 0, "Included": 1})
@@ -35,4 +38,6 @@
 
 df_new = df_trans[["pmid", "doi", "label_included"]].copy()
 df_new["openalex_id"] = None
-df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv("Walker_2018_ids.csv", index=False)
+df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv(
+ "Walker_2018_ids.csv", index=False
+)

datasets/Jeyaraman_2020/compose.py

@@ -2,7 +2,9 @@
 
 key = "Jeyaraman_2020"
 
-df = pd.read_csv("https://osf.io/download/pkc3g/", sep="\t", encoding="windows-1252", engine="python")
+df = pd.read_csv(
+ "https://osf.io/download/pkc3g/", sep="\t", encoding="windows-1252", engine="python"
+)
 
 # rename columns
 df.rename({"Label": "label_included", "Title": "title"}, axis=1, inplace=True)

datasets/Kwok_2020/compose.py

@@ -2,8 +2,12 @@
 from asreview import ASReviewData
 
 # load RIS from OSF into ASReviewData object
-asr_inclusions = ASReviewData.from_file("https://raw.githubusercontent.com/asreview/systematic-review-datasets/97bb9b54331265164c991e9aa5a585bbc6e0fa49/datasets/Kwok_2020/raw/Virus_Metagenomics_in_Farm_Animals-INCLUDED-v2.txt")
-asr_search = ASReviewData.from_file("https://raw.githubusercontent.com/asreview/systematic-review-datasets/97bb9b54331265164c991e9aa5a585bbc6e0fa49/datasets/Kwok_2020/raw/Virus_Metagenomics_in_Farm_Animals-ALL.txt")
+asr_inclusions = ASReviewData.from_file(
+ "https://raw.githubusercontent.com/asreview/systematic-review-datasets/97bb9b54331265164c991e9aa5a585bbc6e0fa49/datasets/Kwok_2020/raw/Virus_Metagenomics_in_Farm_Animals-INCLUDED-v2.txt"
+)
+asr_search = ASReviewData.from_file(
+ "https://raw.githubusercontent.com/asreview/systematic-review-datasets/97bb9b54331265164c991e9aa5a585bbc6e0fa49/datasets/Kwok_2020/raw/Virus_Metagenomics_in_Farm_Animals-ALL.txt"
+)
 
 # set labels and turn into single dataframe
 asr_inclusions.df["label_included"] = 1

datasets/Leenaars_2019/compose.py

@@ -1,8 +1,7 @@
-import pandas as pd
-from asreview import ASReviewData
-
 import urllib.parse
 
+import pandas as pd
+from asreview import ASReviewData
 
 key = "Leenaars_2019"
 
@@ -13,6 +12,7 @@ def unquote_nan(x):
  except Exception:
  return None
 
+
 inclusions = [
  {"pmid": None, "doi": "10.1016/0304-3940(96)12918-9"},
  {"pmid": None, "doi": "10.1016/j.neures.2004.05.001"},
@@ -30,7 +30,7 @@ def unquote_nan(x):
  {"pmid": None, "doi": "10.5665/sleep.2106"},
  {"pmid": None, "doi": "10.1111/j.1471-4159.2011.07350.x"},
  {"pmid": None, "doi": "10.1080/01616412.2015.1114231"},
- {"pmid": None, "doi": "10.1523/JNEUROSCI.5933-11.2012"}
+ {"pmid": None, "doi": "10.1523/JNEUROSCI.5933-11.2012"},
 ]
 
 df_inclusions = pd.DataFrame(inclusions)
@@ -39,8 +39,13 @@ def unquote_nan(x):
 asr_pubmed = ASReviewData.from_file("https://osf.io/download/m523q/")
 asr_embase = ASReviewData.from_file("https://osf.io/download/exm3a/")
 
-asr_embase.df["doi"] = asr_embase.df["url"].str.extract(r"doi\/(10.\S+?)&")[0].apply(unquote_nan)
-asr_embase.df["pmid"] = "https://pubmed.ncbi.nlm.nih.gov/" + asr_embase.df["url"].str.extract(r"pmid\/(\d+)&")[0]
+asr_embase.df["doi"] = (
+ asr_embase.df["url"].str.extract(r"doi\/(10.\S+?)&")[0].apply(unquote_nan)
+)
+asr_embase.df["pmid"] = (
+ "https://pubmed.ncbi.nlm.nih.gov/"
+ + asr_embase.df["url"].str.extract(r"pmid\/(\d+)&")[0]
+)
 
 # set labels and turn into single dataframe
 df_inclusions["label_included"] = 1
@@ -50,12 +55,14 @@ def unquote_nan(x):
 
 # adjust columns and drop missing and duplicate ids
 df["doi"] = "https://doi.org/" + df["doi"].str.extract(r"(10.\S+)")
-df["doi"] = df["doi"].str.split("&", n = 1, expand = True)[0]
+df["doi"] = df["doi"].str.split("&", n=1, expand=True)[0]
 
 # save results to file
 df.to_csv(f"{key}_raw.csv", index=False)
 
 df_new = df[["pmid", "doi", "label_included"]].copy()
 df_new["openalex_id"] = None
 
-df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv(f"{key}_ids.csv", index=False)
+df_new[["pmid", "doi", "openalex_id", "label_included"]].to_csv(
+ f"{key}_ids.csv", index=False
+)